It's hard to give a suggestion without knowing more about the situation(boat
size, water conditions, whatever is is you're measuring, whether or not
you'll be in the water or working from the boat, etc.)
A cheap way would be to just get some sections of PVC of a convienient
length that can be assembled with couplers and taped together when needed.
Use a marker or colored tape to make the measuring marks. Glue a plug on
each end so it will float, then you can attach a line to it and just throw
it alongside the object to be measured.