Boat US and SeaTow give Free MMSI numbers in the US. But these numbers are not official FCC numbers and are not in the international data base. So if your recreational vessel requires a Radio license--as it really might, it you go into Canada, Mexico, Bahamas etc, you need the FCC number, for which there is a fee.
Most US yachts go into Canada, without a radio license--and we all assume that there is reciprocity there...which there seems to be. visa versa...but read on.
Canadian rules are:
Use this application form if the vessel does not require a radio licence and if the radio equipment on board consists of one or more VHF/DSC radios. Radio equipment must be certified under the applicable Canadian Radio Standard Specifications for use in Canada. If the vessel requires a radio license or if additional radio equipment is installed, use the application form for a ship station with a radio licence.
I do not know what the cost of a Canadian's ship radio license is.
If you use your radio, or transit into Foreign waters just like the Americans, you need to have a Ship's radio license. If you have a ship's radio license, ($$ in both the US and Canada), then you have to use a different form for your Canadian MMSI. Now, as a matter of reality do all the boats from the US, or Canada going into each other's waters, get a ship's license--NO.
Ham is easier--there is a reciprocity, and you use just eh prefix for Canada,'s region with the US Call sign, such as VE7/KA6PKB if operations in BC waters.
In the US, the MMSI is free from the FCC--only problem is if you want the internationally recognized MMSI you have to have the Ship's radio license, and this requires several fees--one to be registered to do electronic applications--same for Ham, Marine, Aircraft--so since I already have a FCC number, then I can go and pay the marine license fee, and then get the marine call sign, use ASI A, and the MMSI for international waters. The FCC license itself is 160 for 10 years, and is boat specific. This is needed for any voyage into international waters, as well as Marine SSB, Fixed satellite communication on the boat (not the hand held Sat phones).