The intake size for the stock turbo is 2.75", you can spent as much or as little as you would like installing a filter on this from an eBay special to a closed crankcase breather setup like an airsep brand. Before you go through too much trouble on this, I would inspect the condition of your exhaust side V-band coupling from the turbo to the "can" which connects to the riser/mixer. The rust away and can leak exhaust into the boat eventually. You can dress it up with a file but eventually the lip for the v band clamp gets pretty thin and can rust apart.
I retrofitted mine to a eBay knockoff of the Holster H1C, the exhaust side is 3" nominal v band versus the 2.5" stock turbo so an adapter is needed. The intake side is 3", same as the 210 hp spec Cummins 6bt (non-aftercooled), there are plenty of intake filter options for these. This is why I suggest checking the computer condition of your stock turbo first. You can get a direct replacement turbo but it is about $800-1000 more than what I used.
For the crankcase breather, you can get a filter with a hole and plastic elbow for the breather hose to attach to, just run the hose to a catch jug. Rig up a ventilated catch can or get a walker airsep or SBmar setup. I just ran mine into a old antifreeze jug, doesn't have much blowby at all, especially at the low rpms most of us run at.
I covered the turbo swap in this thread:
Attached is a pic of the stock intake.