The San Juan, like the Colorado, can be run year-round. This may mean running it at 500 cfs, but it can be done.
As for side hikes, attractions, and other river running info for the SJ, a good place to inquire would be the UtahRafters-dot-org website/forum.
As for the boats at San Juan College, my brother rented one last year. It was a decent but older Hyside with a NRS frame and Carlisle oars with oar rights & enough straps to get it rigged (bring more straps for your personal gear if you've got 'em). If you're not a rafter, you may want to go over how to rig the boat with the staff when you pick it up. You'll need to adjust the seat for your height and probably make other minor adjustments to the frame. The only thing I'd be wary of is what they gave us for a "dry box" - kind of like an flimsy over-sized plastic suitcase that didn't really attach to the frame very well & wasn't really sturdy enough for an adult to sit on. I think it was some kind of Army-surplus gear box. Ask about it in advance and if they haven't upgraded their gear over what we had last year, be ready to get some big drybags and eat pringles and make your sandwiches with pita bread or tortillas (life's rough, eh?). Overall, I really appreciate the service they provide and for $120/wk, it's the best deal you'll find - I've got a boat reserved for June and will continue to come back to them for my brother's western boating trips.
Call San Juan College ASAP to reserve a boat - it may be slim pickings for the rest of the summer.
Nothing in the world is more yielding and gentle than water. Yet it has no equal for conquering the resistant and tough. The flexible can overcome the unbending; the soft can overcome the hard. - Lao Tse