My son had Tommy John as a sophomore in high school after a couple periods where his ortho surgeon knew the ulnar collateral ligament was compromised, but hoped that rest and rehab would heal it.
His surgeon is a pretty prominent sports doctor. His theory from when my son was age 13 1/2 and throwing 85 mph was, "Surgery is invasive. People treat it like it's nothing, but it's the last resort. If a young pitcher can possibly heal, that's the first option. I don't want to do surgery on a young pitcher like your son until you both come in here and tell ME it's absolutely time for surgery."
So...resting and rehabbing as you had was absolutely the right thing to do. My son came back both times and felt fine. He actually might have recovered completely entering his freshman year, but his varsity baseball coach overworked him...I didn't step in and raise hell over it...and things went from sore but pitching great to him being really sore. The elbow locked up on him in a tournament in Arizona...so he rested another full summer, etc. He came back as a sophomore and was throwing so well he was going to be the ace of a pitching staff with a kid headed for U of Arizona, you know? So...again...rest and rehab helped.
But...one day in the pen he was warming up to close a game and just knew something was really, really wrong. He came into pitch and he showed the 2 symptoms of a pitcher who's elbow was destablized and in need of surgery...he had no velocity (and he was up over 86, 87, 88 at that point) and he simply could not throw a strike.
After he pitched 1/3 of an inning...he said he wanted to see the doctor. He had surgery a few days later. The doctor said, "There aren't any guarantees that surgery results in a kid coming back 100%...that's why I wanted YOU guys to tell ME when HE wanted surgery."
My son didn't come back 100%. His elbow doesn't hurt, but it wasn't the story we hear when a big leaguer returns. He still has far less velocity and command. His ulnar nerve started pressing against something and he thought he was done, forever, 3 weeks ago. (Turns out that nerve thing is easy to fix in his case.)
So...if YOU think you need surgery. Tell your ortho guy. He works for YOU. All you get on here is conjecture and opinion...but, my son's timing was such that he didn't pitch past his freshman year...a few innings as a sophomore...some innings (not very good) as a junior...a full summer last year and then 17 pretty OK innings this year before the nerve deal.
It's your arm...your career...so, make the best decision you can. At some point...a long rest and rehab means you're not a college scholarship kid or a draftable kid...but, the important thing is getting to pitch in high school, I think.