Each has its pros and cons. While aluminum will corrode in chlorinated water, it is much lighter than brass. Brass doesn't corrode, per se, but it is far heavier than aluminum. This weight might end up hurting you, though. This is because you'll need to keep your weight as low as possible to maintain stability (mostly surfaced) and with big blocks of brass as end caps, your weight will be pretty high. Virtually all model submarines require weight to be added with the keel the most obvious place. Using brass, your boat's overall weight will reduce the amount of weight you'll need in the keel. This can be offset to a large degree by the use of foam, however, but you'll probably need quite a bit and you'll still have to add weight in the keel.
Realizing the faults inherent with acrylic, I've been very successful using 3/8" thick acrylic as end caps with zero ill effects. The thicker the piece is, the better (to a point, anyway. Use a very sharp tool and leave a small radius instead of sharp corners and you'll be home free.
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