Pokemon-go – Can all gifts contain Eggs

Not really, no. The only Pokemon that would be considered to be 'only hatched from an egg' are the region-restricted Pokemon. But, even then, if you were to travel to one of those countries, you could of course catch those as well. The region-restricted Pokemon can be seen here: What are the regional Pokemon?

Edit: I feel it is important to add that this is still a pretty hotly debated fact. There was a survey done which claims to conclude that out of approximately 40,000 hatched eggs, none of the Pokemon were region-locked Pokemon. However, there are some people who claim (with evidence) that they have hatched region locked Pokemon. Some of these people even claim to have spoken to the person who created the aforementioned survey, only to have that person dismiss their claims as lies or 'hacking'.

So, right now, I am leaning towards that it IS possible to hatch region-locked Pokemon, however, there is yet to be 100% conclusive evidence either way. You can see some of the threads on Reddit where users have made claims for both sides.

Edit 2: Just to be clear, the answer to the actual question at hand here still appears to be no, the edit above is just some additional information, some of which may be a bit beyond the scope of this question.

Your eggs not hatching is independent of your mode of transit. This means that whether you are on a boat or not does not affect your eggs hatching. What does affect distance being recorded is connection to the internet, travel speed, and being soft banned.

Connection to the internet - when you visit a lake, often you are going to remote places with no wifi and poor cell coverage. Thus, if the app cannot accurately track your location and connect to Niantic servers, you distance will not be tracked for your eggs. Check your available networks and reassure that you still have ample data coverage on your boat.

Travel speed - it is now confirmed by a large number of players that traveling too fast can affect egg hatching. It is a general consensus among players that the maximum speed for hatching eggs is ~10-12mph (15km/h is about 9.3mph), so perhaps consider slowing down, as you are traveling at just about the maximum speed for tracking egg hatching distance. You can reference this question for more about speed: How fast can I travel?

Soft ban - if you have been recorded for cheating via GPS spoofing or any other form of cheating, you will likely be soft-banned (or banned for a short amount of time). When you are soft banned, you cannot catch Pokemon (they all run away), some distances don't track, and you can't get items from PokeStops. Refer to this question for more about soft bans: Why can't I catch Pokemon in Pokemon Go anymore?

In addition, if it worked yesterday and doesn't work today, it might just be a server issue with Niantic, and will resolve itself in time. It's a bit hard to conclude anything with only 24 hours of evidence, but wait a little longer and try again. If your distance is still not tracking, consider one of the above prognoses.