Caveat: Janitor says paycheck and paid much more. He does not say paid more per hour. Both are likely salaried and the p/h below is for comparison of their biweekly paycheck.
Consider that Sacred Heart is a Teaching Hospital, and JD is a resident at the time, a non-licensed medical student whom the hospital is basically investing in. He's not paid a regular doctor's salary.
With some quick google checks, the average Medical Resident has a salary of 55,000. (26.50 p/h assuming 40 hour work week. Effective pay rate may be lower depending on hours worked):
Average residency salaries increased from $51,000 in the first year after medical school to over $60,000 after the fifth year. According to a recent commentary in the New England Journal of Medicine, when adjusted for inflation, resident compensation has not changed in 40 years.
The average hospital custodian makes much less:
Hospital Pay. The average hospital custodian earned $12.49 per hour as of May 2011, according to the U.S. Bureau of Labor Statistics. This equals a yearly salary of $25,980 for custodians working a 40-hour week all year.
Of course, Janitor does more than just clean. He's seen doing repairs. He's seen bossing other janitors around. So he's more like a Facilities Supervisor. Not quite a manager or mid-management, but not a basic custodian:
The median annual Facilities Maintenance Supervisor salary is $74,404, as of July 29, 2016, with a range usually between $64,323-$84,750, however this can vary widely depending on a variety of factors.
So yes, it's likely that Janitor was making more.
P.S. Medical students have hundreds of thousands in student loans, and the medical industry is brutal. Not all doctors make even 6 figures. Which is why Elliot bailed on Sacred Heart for the For-profit hospital, increasing her pay by much. It's a whole thing between her and the Dean of medicine Kelso.
Later in the series, after firing and rehiring Janitor, he gets a pay raise by saying his new paycheck is half of what he used to make. So he's making much more, though JD is a Doctor at the time. The pay difference probably didn't change.