"I travel by boat."
Translation:Ninasafiri na boti.
I feel like it's largely dependent on who taught you. I had a Swahili teacher back in high school (and I think primary school) who was adamant on using "kwa" because according to them, using "na" implies that you travel together with the boat, as opposed to on it. I typically use kwa for 'with' and 'by' if it's an item/appliance I am using to accomplish something (like utensils, tools, travel modes, etc).
Grammatically, in my opinion/experience, 'kwa' is more correct in this context. 'Na' would be used with things you bring with you, which in this case you're travelling together with e.g. 'Ninasafiri na virago vyangu' (I travel with my belongings)