well, the simple solution is to put a rope anchor dead center on the back of another boat and attach it to a matching one on, preferably, the front of the boat you want to tow.

If you want a little more control, put a winch on the back of your tow boat so you can adjust the length.

If this won't work, for example because your disabled boat has no rope anchors, you can build a grappling block. Start with an electric cable anchor on one end, mag-alls on the other end. In the logic section of your editor you can connect the electrical cable to a winch (the bottom tab, labeled 'rope'; if you attach a 'rope' to an electrical cable anchor it will be an electrical cable) and set an activation signal to pass through the winch (a pink dot from a button connects to the matching circle on the winch, then the pink dot on the winch connects to a circle on the electrical connector, and a pink dot on the connector connects to circles on each mag-all.) You can make a variety of shapes, the simplest is just one mag-all and a common solution is a line of three mag-alls.

If you really want to get fancy, and you can afford a big enough boat, you can actually build a tow bar on the back of it. The tow bar is basically a big arch over the back of your tow boat (I say arch to get the idea across, but it doesn't have to be curved) that has winches on the top of it. Provided the interior dimensions are taller and wider than the boat you're trying to move, you can then use the winches on the top to actually heave your disabled boat out of the water and onto your hauling boat. You can do this with just the tow bar if you build it on robotic pivots so it can swing in; otherwise you'll need a winch further forward on your hauling boat for the final pull. Once it's there, ideally you'll have some mag-alls or winches with tow blocks on your deck to secure it. You could even use some pivots or linear tracks to form a little mag-all cradle for it.

Or, in the final extreme, you can lower grappling blocks from winches on a large helicopter or VTOL and actually fly your disabled boat wherever you need it to go. Well, as long as it's not super massive anyway. One helicopter that has a solid amount of lifting strength while still being stable and controllable is the MRR5 Gnisir on the workshop. You may need to add ventilation to the cabin if you use that one though, like most workshop creations it was last updated before space (I think) and may not include cabin ventilation as it wasn't needed back then.