cbrackney, if referring to the City Wonders tour linked above, I believe you meant to say that it does NOT mention St. Peter's? No it doesn't, and you won't be able to access it from inside the museums on that tour...which isn't really a "tour" of the museums at all as all it does is get you inside and directly to the Sistine early. It is NOT a guided tour of other parts of the museums or St Peter's. To visit the basilica, you'd need use the regular exit for the museums, walk outside 'round to St Peter's Square, and get into the security line for the front entrance. That line can be very long but moves steadily.
Tours of the museums which do include the church access it via an internal passage at the back of the Sistine which is reserved for guided tours. The exception would be Wed. mornings when the Pope is holding Papal Audiences, or other random, major services in the basilica which closes it to visitors. For instance, the Pope is holding a mass there at 9:30 on Holy Thursday (April 9th this year) so the church would be off limits to tours and other sightseeing visitors before and during the service.
Editing to add: this is an example of an early-entrance guided tour which includes the basilica (exceptions mentioned above apply.) There are some other companies which have similar so this is just one example, and it has been particularly popular with RS posters who've taken it.
https://www.walksofitaly.com/vatican-tours/pristine-sistine-chapel-tour/