The Montgomery GI Bill does indeed cover non-degree continuing education certificate programs. This is one of the advantages of using the MGIB over the new Post 9/11 GI Bill; the newer bill covers primarily traditional degree programs. But the MGIB is a lot more flexible. Look on the VA’s Weams Institution Search page under your state, and see if your school is covered (which it is).
To find out if a specific certificate fee is covered by the GI Bill, go to the Veteran’s Affairs department’s Weams Licenses/Certifications Search page. Look under your state, and search for the program. If it shows up, it is covered. The search will also show you how much the GI Bill covers for each license or certification.