The Daily Mail article actually did a good job of providing a source of the "The Shame of Our Prisons: New Evidence" from the New York Review of books which provided a good jumping off point. Doing a fair one to one comparison for this can be tough due to reporting rates, namely that it is under reported. In this case though, the Bureau of Justice Statistics published the "Sexual Victimization in Prisons and Jails Reported by Inmates, 2011–12" report that summarized the findings as follows:
Among the 91,177 adult prison and jail inmates participating in the
NIS-3 sexual victimization survey, 3,381 reported experiencing one or
more incidents of sexual victimization in the past 12 months or since
admission to the facility, if less than 12 months. Since the NIS-3 is
a sample survey, weights were applied for sampled facilities and
inmates within facilities to produce national level and facility-level
estimates. The estimated number of prison and jail inmates
experiencing sexual victimization totaled 80,600 (or 4.0% of all
prison inmates and 3.2% of jail inmates nationwide) (table 1).
Note that the report does not distinguish between male and female for the 97,177 adult prison and jail figure, but it does provide the following detailed breakdown,

For the same year, the FBI Crime in the United States 2012 report for forcible rape that,
There were an estimated 84,376 forcible rapes reported to law
enforcement in 2012. This estimate was 0.2 percent higher than the
2011 estimate, but 7.0 percent and 10.1 percent lower than the 2008
and 2003 estimates, respectively. (See Tables 1 and 1A.)
where forcible rape is defined as,
Forcible rape, as defined in the FBI’s Uniform Crime Reporting (UCR)
Program, is the carnal knowledge of a female forcibly and against her
will. Attempts or assaults to commit rape by force or threat of force
are also included; however, statutory rape (without force) and other
sex offenses are excluded.
Which implies that on a basic level that the reported rate of forcible rapes against females is slightly higher than the aggregate 80,600 estimate for prison and jail populations across males and females. However, since the FBI data is limited to females we are going to need to look for a more inclusive source of data.
The CDC has the National Intimate Partner and Sexual Violence Survey which breaks things out by gender, sexual orientation, and on the basis of lifetime and 12-month rates. For the "Prevalence and Characteristics of Sexual Violence, Stalking, and Intimate Partner Violence Victimization — National Intimate Partner and Sexual Violence Survey, United States, 2011" the following was reported,

This is where it is important to note the methodology for the NISVS from their PDF report,
The National Intimate Partner and Sexual Violence Survey is a national
random digit-dial telephone survey of non-institutionalized English-
and/or Spanish-speaking U.S. population aged 18 or older. NISVS uses a
dual-frame sampling strategy that includes both landlines and cell
phones. The survey was conducted in 50 states and the District of
Columbia and was administered from January 22, 2010 through December
31, 2010. In 2010, a total of 18,049 interviews were conducted (9,970
women and 8,079 men) in the U.S. general population. This includes
16,507 completed and 1,542 partially completed interviews. A total of
9,086 females and 7,421 males completed the survey. Approximately
45.2% of interviews were conducted by landline telephone and 54.8% of interviews were conducted using a respondent’s cell phone. The sexual
orientation of the sample included 96.5% females identied as
heterosexual, 2.2% bisexual, and 1.3% lesbian. For males, 96.8%
identied as heterosexual, 1.2% bisexual, and 2.0% gay.
Thus it should be noted that incarcerated persons would not have been included in the NISVS data and I didn't see anything that indicated former incarceration status of the persons surveyed so that can not be taken into account either. However, given the basic summary findings of the NISVS,
In the United States, an estimated 19.3% of women (or >23 million
women) have been raped during their lifetimes (Table 1). Completed
forced penetration was experienced by an estimated 11.5% of women.
Nationally, an estimated 1.6% of women (or approximately 1.9 million
women) were raped in the 12 months before taking the survey.
An estimated 1.7% of men (or almost 2.0 million men) were raped during
their lifetimes; 0.7% of men experienced completed forced penetration.
The case count for men reporting rape in the preceding 12 months was
too small to produce a statistically reliable prevalence estimate.
However, it should be noted that there are limitations associated with the NISVS data,
The findings of this report are subject to at least five limitations.
First, the overall response rate for the 2011 NISVS survey was
relatively low (33.1%). However, the cooperation rate was high
(83.5%), and multiple efforts were made to reduce the likelihood of
nonresponse and noncoverage bias. These included a nonresponse
follow-up in which randomly selected nonresponders were contacted
again and offered an increased incentive for participation as well as
the inclusion of a cellular telephone sample. Second, although NISVS
captures a broad range of self-reported victimization experiences, it
is likely that the estimates presented underestimate the prevalence of
sexual violence, stalking, and intimate partner violence (18). Victims
who are involved in violent relationships or who have recently
experienced severe forms of violence might be less likely to
participate in surveys or might not be willing to disclose their
experiences because of unresolved emotional trauma or concern for
their safety, among other reasons. Third, a telephone survey might be
less likely to capture some populations that could be at higher risk
for victimization (e.g., persons living in nursing homes, military
bases, prisons, or shelters, or those who are homeless). Fourth,
self-reported data are vulnerable to recall bias because respondents
might believe that events occurred closer in time than they did in
actuality (i.e., telescoping), and this type of bias might
particularly affect 12-month prevalence estimates. Finally, follow-up
questions were designed to reflect the victim's experience with each
perpetrator across the victim's lifetime and there were limitations
associated with how these questions were asked. Respondents were asked
about the impact from any of the violence inflicted by each
perpetrator. Therefore, the impact of specific intimate partner
violence behaviors cannot be assessed. Also, because victims' reports
of the age and relationship at the time any violence began with each
perpetrator were used, it was not always possible to assess the age or
relationship at the time specific types of intimate partner violence
occurred.
Although based upon review other reports associated with the Wikipedia survey on the topic it appears that these limitations likely apply to all mass surveys of this topic.
On the assumption that most rapes go unreported as indicated by the NISVS data I find it to be implausible that even with BJS prison statistics that the rate of rapes of males would be higher than for females. One thing to note though is that the BJS information seems to indicate that most victims in prison are repeatably raped while the NISVS data seems to indicate singular reports so that might be a distinction that would need further investigation.