Best way to get from San Marco to Marco Polo Airport?

It depends on what you mean by best.
Usually the faster way the more expensive.
Basically three options.
1. Water taxi is the fastest, but it's about €120
2. Alilaguna boats (sort of a bus on water) is more reasonable but not quite as fast (Google alilaguna)
3. Vaporetto to Piazzale Roma, then ACTV bus or taxi.

There's also a shared water taxi for about 25 euro per person. They pick up at San Marco but are a little hard to find.