I ran a very successful SR3 campaign which totally ripped off the anime Black Lagoon. Luckily none of the players knew it.
For a real, independant pirate campaign
I would do the following:
You need a map. Make it big, either buy a large map of, for instance, SEA, or the gulf of mexico, eastern Africa, or whatever, or print one to make a large map covering the entire game table. Then paint in some shipping lanes, ports of interest, pirate havens, etc.
IMHO for pirating to be interesting and self-motivated, you need a gamey mechanic to locate and pick the quarry they could conceivable target. So you can't just go ahead and cruise about while looking for ships ripe for the picking, because that just results in random fights and then looting stuff. I would very precisely locate the current position of the PC boat on the map (using a pin, for instance), and also other boats within radar range, or that they have knowledge of. I would also keep track of - hidden from the players - any serious opposition they might be meeting up with, keeping in mind distances, speeds, locations, headings, response times, etc. Using pseudo-naval tools - for instance a compass to track radar range, travel legs, etc., will keep things visually tangible.
The PCs might use the matrix to find out about cargo ships or convoys which are about to take a shipping lane in their vicinity. Or they get hints from paid off harbor officials, etc, which ships might be lightly guarded, carry a valuable cargo, etc.
You also might want a game clock, after every increment of which you update positions. That way you can have real chases. Keep in mind that at sea there are few places to hide, and the distances at which people come aware of each other are rather large. So a chase could take place at several hundred miles distance.
Another interesting angle is always competitors: If the PCs start out as the new kids on the block, then likely as not there are established pirate gangs in place who will brush with them. This might provide more adequate challenges initially, before they come in contact with an Ares cruiser looking for a kidnapped ship.
And finally, you need to work out a convenient mechanic of dealing with income and costs. The spoils of piracy might be quite large, but the running costs could also be high - in the 6th world at least, where companies don't easily pay pirates, because human resources are a much cheaper asset than nowadays. I've had to deal with the problem that the runners ransomed a ship off for 2 million or so
, which is a quite a hefty sum, but you need to deal with that in some way. This is what modern pirates do, so simply saying "no" probably won't satisfy them. There must be high running costs - bribes to authorities, appeasement money to local warlords, equipment, fuel, supplies, information, etc. Also, I would do away with static availabilities - you probably want the common AK or RPG-launcher to be easy to come by, but ship-mounted railguns rather less so. Perhaps it's a good idea to assign availability and price mods to certain groups of goods per port - that also makes for a good smuggling opportunity - if at one port an item is easily available, but scarce at another, you suddenly have a hook. Obviously you need to revise the buying and selling mechanics a bit - if it's impossible to sell stuff for profit, then it makes no sense to try.
Then there even considerations that come first: Where do the PCs get their ship, and what kind is it? Do they just buy a rubber dingy and then capture a ship to use as their mothership (like current pirates would)? Or do they buy a mothership? Do they attack with that, or do they use small boats? What is their threat possibility? Most small arms can't harm a large cargo ship, but of course in SR it might be easier to enter one while under way. A crew of runners might do so without even getting noticed. Etc...
These are my thoughts, considerations and suggestions on this, so far. By no means complete, obviously.