If it were mine, I'd prefer to have someone that only does boat repair to work on it, not an auto body shop. $3500 plus does seem high, but if it's not something they do every day, that may be why they are estimating it high. Could not tell you what it should be but gelcoat repair is labor intensive and depending on what a shop chargers per hour, can run high for even small repairs.

Anyway, sucks to have that damage. Best of luck.