Most people coming to Tepotzotlan don't stay just in this city, but also visit some other towns inside the municipality, at least two of them has nice colonial churchs and you'll find information about them on the tourist information posts in Tepotzotlan's main square.
I visited the location most travelers chose, a large aqueduct built by the jesuits and known as "the arcs of the site" you can read about it on my San Francisco Magú page.
After visiting the museum it is possible to wander around the gardens of the college, as in the temple the only way in is trough the museum, this gardens are very well taken care of and there are also some old statues left there by the jesuits, most visitors don't visit the gardens are walk only a small zone of them so if you want you can go away from the people and have a very relaxing walk.
Appart from the college and the convent, the jesuits had a church, and it still remains, it is no longer used for any religious activity, but it is open to the public, it is one, and probably the biggest attraction of the museum, paying the ticket to the museum is the only way in since all the other doors are closed, but there is no extra cost, so while you're visiting the museum you'll see this fantastic temple.
The best feature of the temple are the baroque altarpieces, most of them were designed in the XVIII century and they are in a great state os conservation, it is very worthy to see them.
My pictures are not very good since flashes are not allowed and there was no place to support the camera, but do a image search on the internet and you'll surely find some better pictures of the altarpieces so you can see how beauty they are.