Parking in the Swamps is pretty safe, although it's not a good idea to part at the closest possible spot. Due to how zones load in, if you see a Swamp in the distance, beeline straight towards it, and then dismount immediately, you're probably walking into an undead army.

However, if you do a bit of circling around a Swamp before picking a decent-looking parking spot, you're going to have far less unwanted visitors. I'd argue that taking the boat down afterwards is your best bet; better to take down your own boat and guarantee that you collect all of the mats used to make it, than have something else destroy it when you aren't there, which might prevent you from collecting all the mats (Iron Nails sink in water, for example).