Mike,
I know this may be long winded but..... Once Algae is in your tank you have one of two choices, kill it or starve it.
Kill it, you have to treat with a biocide, this stuff is very dangerous for you to use, think totally suited up and don't get any of this on your skin or breathe it either. This difficult for an individual to purchase.
Starve it, All the water moisture has to be removed from the fuel and kept out long enough to starve the algae, I can't tell you how long that is , it depends on the algae, probably 3 or 4 weeks ( although forever would be good) Go to a NAPA type parts store and buy fuel additive that removes moisture, in ME anyone that sells diesel will have the stuff, my favorite brand is HOWES but any will work. Drain the water out if you can ,replace filters and run engine. You may want to consider a fuel/water seperator for your boat if you don't already have one. Keep your fuel tank full and use the correct amount of fuel conditioner for several weeks and your problem will be solved.
I might add here a test for algae or simply sludge, drain some out of the filter and smear on a cloth. spray this gunk with a degreaser or starting fluid. If it dissolves it is just gunk, if the cleaner does nothing to it , it is algae.
That's my "short" answer!!