I am no expert, nor an attorney.
Waterways can be state, national or international. For your purposes, I assume we are talking about inland waterways and not offshore (not past the COLREGS demarcation line, or beyond the 3 mile or 12 mile limits). In that case...as far as I know....that is state land (submerged lands) and under state jurisdiction.
And you are further compromised by being on a boat. The USCG has jurisdiction over all vessels of all types, that are US flagged...anywhere in the world. As far as I know, it is my personal understanding that unlike being in your home, the USCG can board your boat at any time, anywhere for any reason. As far as I know, the USCG needs no probable cause, they simply conduct a safety inspection.
If a state officer wants to board your boat, all they have to do is ask a USCG or Homeland Security vessel to assist.
Just my 0.02...YMMMV....nothing above constitutes anything that may be construed as legal advice. I am in no way responsible for what you may do with this advice.
And...btw...if a CG or LEO asked me a direct question, regarding weapons or anything else aboard my boat, I ...personally...would give them a straight, honest answer.