You're right, there are several options.
First let me say that with a species such as a boa, lining the floor with something durable and easy to clean is always a good idea. Vinyl flooring, FRP board or PVCX are all good choices. PVCX is especially good if you want to incorporate "belly" heat into your cages.
I would do this regardless of what sealer you use. Unless you ended up using an epoxy.
The sealer itself should probably be limited to an oil-based product or an epoxy. For a boa I would avoid water based products.
If you want a clear finish you're either limited to the oil based polyurethanes or epoxies. All of the epoxies are difficult to use and have nasty solvents. Once exception to this is Envirotex Epoxy - expensive, but my favorite sealer.
If a solid color is okay then you can use oil-based paints.
Understand that if you only seal the floor and do not use a covering of some sort you will likely have to go in a touch up or redo the paint every year or so. This will likely be the case with both the oil based paints and polys.
The two part epoxies will be a much longer lasting finish.
Here is a picture of a cage sealed with envirotex epoxy. There is about $50 worth in this 4'x2.5'x4' cage.
