I'd say the 3g. tank...
Why?
Less room for it to take up, and less weight to deal with. Cheaper to FILL... :lol:
Seriously, most fuels these days are an ethanol blend. Ethanol will draw more moisture into the fuel than straight gasoline. Legally, the mix is supposed to be no more than 10% ethanol--but in reality, there have been stations found that were serving up to 43%.
Since boats tend to live outdoors or in the water, moisture can be a big issue.
A smaller tank means it's easier to pull out of the boat and put in garage (away from moisture). It also means that you're less likely to leave a half-full tank sitting in the weather, or leaving sit all winter to attract moisture or gum up (varnish).
I have a 20hp yamaha on my alaskan smoker aluminum, and it'll easily go all day on 3gallons. The way I fish, it'll last a handful of trips. No point in a bigger tank, IMHO.