I'm reading through Bernstein's The Poly1305-AES message-authentication code.
The MAC is predicated on 16-byte block ciphers like AES and produces 16-byte authentication tags. However, Bernstein does not really discuss the block cipher's key sizes, other than to state its a 32-byte key comprised of a 16-byte key and a second 16-byte string r.
I presume Bernstein selected AES-128 because it met security requirements with the most efficiency (i.e., AES-128 is faster than AES-256 because it uses fewer rounds, among other stated criteria). (Bernstein talks about the selection of other parameters, like r, in the section Design Decisions).
If one desired, could Poly1305-AES be used with AES-256? In this case, a 48-byte key would be used.