That’s a tough one.
We don’t have much in the way of hard textual evidence, and the Riverlands in general are really tricky because they underperform in power given their population and relative prosperity. What we know is that A. the Mallisters have a fleet of six longships and two war galleys (which is not a large fleet, but not a small one either), and B. were able to hold off the main force of the Ironborn during Greyjoy’s Rebellion.
I did an estimate in the past and said that I thought 4,000-5,000 was a reasonable figure. It’s not the most solid estimate I’ve ever done, for the reasons stated above, but I don’t think they’re particularly weaker than the Freys, given their geostrategic location, its economic advantages in trade (to the extent that the Freys are wealthy, most of their trade has to pass through Seagard), and the historical evidence.
As to Seagard itself. It definitely is a port – Theon sails to Pyke from Seagard on a merchant ship from Oldtown – although it’s definitely a port town at most. As for why it has trade despite the Ironborn presence, keep in mind Ironborn piracy has lapsed for long periods of time (several thousand years), and that the presence of pirates tends to presuppose trade since pirates don’t bother to sail where there’s no one to rob, because often geography means that ships have to sail through a given region no matter what. (Think about the real world example of huge amounts of shipping going through certain pirate-infamous locations like the Caribbean or the South China Sea or the Horn of Africa….)

In this case, if you’re going to trade from the North, the Vale, or the Riverlands to the Westerlands or from the Westerlands and even parts of the Reach to the same, it’s faster to go through Seagard and trans-ship down the Blue Fork or portage over to the Kingsroad and then over to White Harbor than to sail all the way around the continent or to take it overland. Not safer, but faster, and since time literally is money when you’re talking about transportation costs and their relationship to profit margins, a lot of folks will go with the faster option.