Most ocean boats say bay boats or pontoons have real issues with garage doors since they are typically tall.
Boat garage door height.
As with the garage length this will depend on the height of your pontoon and trailer considering the bimini too.
Garage door height is a key limiting factor for most boats excluding bass boats.
As a rule of thumb you should have at least a foot of clearance for safe movement and storage when you back the trailer and boat back in to the garage.
Bass boats are generally very low profile and only power poles if applicable fishing seats and huge outboard motors ever come close to not clearly.
But do not have to put the tower down and have plenty of room to walk around and even store stuff behind the boat.
For example for a 11 6 boat on a trailer you might want to go with a garage door dimensions of 12 foot high and at least 10 foot in width.
If your boat is above a certain height you need a permit to tow it.
To cover all possible boats that you can tow without a permit than a garage of about 14 7 feet high would cover all the bases.