Actually, the rules for pulling over a car and a boat are completely different. The MP (or Coast Guard et al) do not need ANY reason at all to stop a boat and check it out. Here is one RSA that I found that mentions the matter. There are federal laws as well that essentially say the same thing that apply when in Coast Guard patrolled waters.
270-D:6 Inspections. – All vessels afloat on public waters may be inspected by the commissioner or his duly authorized representative, to determine their seaworthiness and safety equipment at any time. No person shall allow any vessel which fails to pass such inspection to be used or operated on the waters of this state until brought into compliance.
Notice that it says "at any time" and that there are no prerequisites.
Here is a link to the CG rule:
http://uscgboating.org/safety/fedreqs/law_board.htm
Ken