What counts as a modern MTB equivalent

Are modern special-forces raiding craft the equivalent of Second World War MTBs and E-boats?

Only partly; their size and speed are similar, but an armed CB90-type combat boat is closer in mission and weapons to the wartime attack craft.

Modern special-forces craft share the speed, small size, and littoral operating environment of MTBs, PT boats, and E-boats. Most raiding craft are not armed or organized to deliver the same anti-ship striking power, so the analogy only goes so far. CB90-type combat boats are a closer relative because they combine troop or patrol utility with a more substantial weapons platform. Visual similarity should not obscure differences in mission and armament.