What ever you do, don't use brass fasteners on a boat, especially on one that is on salt water.... the brass will de-zincify and then you will lose your ports. I would go with silicon bronze fasteners if the ports themselves are bronze, as you'll have the least problems with galvanic corrosion between the fasteners and the ports.
Both plexiglass (acrylic) and lexan (polycarbonate) will work for ports, but the Lexan will be far stronger. You need to make sure you get Lexan with a UV-protective coating and preferably a scratch resistant coating as well.
What you bed them with may depend on whether you go with plastic (acrylic or polycarbonate) or glass. Polysulfide-based sealants will attack lexan or plexiglass, polyureathane-based ones will not. I would bed them with 3M 4200... since it is very likely that you will have to replace them at some point in the future.
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You know what the first rule of sailing is? ...Love. You can learn all the math in the 'verse, but you take
a boat to the sea you don't love, she'll shake you off just as sure as the turning of the worlds. Love keeps
her going when she oughta fall down, tells you she's hurting 'fore she keens. Makes her a home.
—Cpt. Mal Reynolds, Serenity (edited)
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Still—DON'T READ THAT POST AGAIN.