How do I get off the boat?

As with most places in Mirror's Edge, you shouldn't be sticking around to just kill or incapacitate bad guys and can generally just avoid them all.

After leaving the van, shift over to the left and down the side to the other garage area (where all the bad guys are). In the back left corner, there are two trucks that you can use to get up. The quick route would be to 1) wallrun, 2) jump to pipe, 3) jump to duct, 4) jump back to upper duct. Easier is to just go up the pipe.

If you can't do it extremely fluidly, the guys with guns will rip you up, so if you can take out a few of them, it will be much easier.