Yes there are regular boats
There are 2 or 3 lanchas in each direction each day from Punta Gorda to Puerto Barrios, and all will put a bike or 2 in the boat if they don`t have too many passengers. My brother and i paid BZD100 (USD50) per bike, plus normal fee for ourselves on the 4pm boat from Punta Gorda. Most people wanted to go in that direction on the 11am and 2pm boats, and so the guy operating the 2pm boat wanted BZD150. Takes about an hour.
Strangely the exit tax per person was only BZD6, whereas at the other borders the border staff and other travellers said it was BZD40. The customs girl there simply did an exit stamp for the bikes, and once back in Guatemala we presented ourselves to immigration in a nearby street, but didn`t worry about finding the customs building for bikes. And upon exiting Guatemala i just pretended i didn`t understand the SAT/customs guy and told him "cheers mate" and we rode off. He didn`t seem to care that much anyway.
We were already in the south of Belize after attempting to cross illegally into Guatemala via the SW corner of Belize, but after spending hours crossing the river with steep muddy banks and along horse tracks etc we met a lot of military! So that way isn`t possible, even on the walking track.