I suspect that might be based on estimates using as proxy the US seizures of fentanyl at borders (points of entry more precisely). If we use that method, the claim is only nominally correct, i.e. in terms of quantity of cut product. If product purity is taken into account however, shipping by package/air (supposedly directly from China, but this bit is unclear as to the certainty) seems to take the first spot. From a RAND report/testimony.
Seizure data at ports of entry offer some insights into the dimensions of illicit imports. CBP
reports seizing synthetic opioids, including fentanyl, at land points of entry and checkpoints on
the southwest border, as well as at mail and express consignment facilities and other air ports of
entry. Table 1 shows that in FY 2018, seizures of fentanyl near or at the border ports of entry significantly outweighed those at mail and express consignment carrier facilities. However, after
adjusting for purity, almost 70 percent of fentanyl seized by CBP in FY 2018 arrived by air,
mostly at mail and express consignment carrier facilities. Analysis of FY 2017 seizure data
reports a similar breakdown. Law enforcement and congressional investigations have suggested
that many of the packages at mail and express consignment facilities originate from China. If
CBP seizures represent the true nature of trafficking patterns, then these preliminary calculations
support law enforcement’s conclusion that China is an important source country of illicitly
manufactured synthetic opioids.

Frankly I find it pretty weird that they cannot be certain where packages get mailed from, at country-level granularity...
It seems however that there may have been a trend change in 2019; a news piece from July says:
The number of drug seizures involving high-purity fentanyl sent via mail from China "dropped precipitously" this year, according to Thomas Overacker, the executive director of the Office of Field Operations at U.S. Customs and Border Patrol.
Only several pounds of fentanyl have been intercepted this year at U.S. mail facilities and airports, predominantly originating from China. "Most of the illicit fentanyl" entering the country "does so at ports of entry along our southwest border," Overacker told members of a congressional subcommittee Tuesday.
It's possible that the Atlantic piece (which is from August) may have relied on this newer info/testimony for their claim. I guess we'll have to wait and see year's end DEA's summary/report for a more definite, numerical conclusion.
The same news piece from July offers some possible reasons behind this trend change, again citing some officials:
The shift from China to Mexico is very recent and largely the result of successful drug control strategies implemented in the past two years.
Specifically, officials cited Beijing's decision in May to criminalize all fentanyl-related substances following U.S. pressure. The move led to a decline in the number of Chinese vendors willing to export fentanyl products, according to David Prince with Homeland Security Investigations' transnational organized crime office. [...]
As a result of requiring data on the sender, recipient and the contents of an international parcel, as well as new technology to scan packages, the postal service saw a 1,000% increase in the number of parcels seized containing synthetic opioids between 2016 and 2018. Domestically, the agency saw the number of opioid parcel seizures increase by 750% in the same timeframe.
In 2019, USPS statistics suggest that international seizures are down and domestic seizures are trending up. "This shift may suggest synthetic opioids are increasingly entering the country through means other than international mail," Chief Postal Inspector Gary Barksdale told lawmakers.
If one can offer a better answer, I'll accept that of course.