First off, you are very fortunate, that you have "very good offer from a school" There are a lot of kids out there that would love to trade places. Unfortunately, as you mentioned the timing of this surgery couldn't come at a worst time as far as the NLI signing period is concerned. The summer between Jr and Sr year is definitely the most important for College recruiting. But its not a complete Deal breaker. Most people in baseball realize TJS is now a part of the game and recovery rates are very high. So as a Catcher who's arm is very important, get the surgery ASAP, because his senior season is already in jeopardy at this date. (recovery is a year for throwers) Recruiters who have seen your son will take into account his past performance. If he's really that talented they will know he'll recover. Its the ones who have not seen him previously that probably will pass. So your options may dwindle for the NLI signing period. But as a very influential person in baseball told me. "You only need one (option/team), to like you". I highly suggest talking to his first choice school, and see if any interest exits. If it does, then be completely honest, because it will become known very quickly as your son is "missing" from the summer scene. Call and talk to the school who has made the offer. Obviously they've seen his talent already, and probably will stay with the offer. Then weigh your options. The world has not ended, just the path has an unexpected curve, which may eventually open new vistas.
I've been there as, both my son's had similar situations as seniors in HS, and both are now in the minors and recruiting is but a memory. (thank goodness) If you would like details PM or (dialog) me..