The two Syrian men, aged 26 and 27, were among the 90 survivors of the tragedy, some of whom were filmed being pulled to safety after clinging to wreckage in rough waters.
The suspects were to be brought before a prosecutor later in the day, the harbour police said.
The boat had set out from nearby Turkey with 93 migrants, mostly Syrians.
The harbour police said they came to the rescue of two other stricken migrant boats in the Aegean Sea Tuesday that were carrying nearly 100 passengers between them.
There has been a surge in migrants trying to reach Greece's Aegean islands from the Turkish coast in the last 10 days, mirroring the swell in perilous crossings from north Africa to Italy.