On taking a sub: (note, this is about how HARD it is, not on feasible ways to do it
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It's a lot easier to find a surface vessel at sea than it is to find a sub. (see also: Hunt for Red October) Satellite tracking, etc -- great if you can see it, hard if it's underwater. I'm also sure that SR-era subs are even more stealthy than current best-breed submarines, due to the technology curve growth for detection (and the resulting arms-race of stealth tech).
I don't think that even the naval command has a good idea of where a sub is on patrol, more than a general "Oh, they're somewhere near section 2515...". So, your chances of being able to rig a rendezvous is Reaaaaaally slim. Couple that with the fact that no sub skipper in his right mind is likely to surface anywhere near another ship under normal circumstances.
However, that does sound more doable than taking a ship from port or within a battlegroup.
So, I'll assume that the team wants an SSN (as someone else said, a nuke-boat is generally ... a bad idea.) Thus, your initial objectives seem to be:
1) be able to FIND the ship, or arrange for it to go someplace prearranged.
2) be able to remove the ship's crew (life rafts, helicopter, elemental spirit ...
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3) survive stealingthe ship: i.e., no one's gonna find/track/kill you.
Subs seem the best for #3 - since you can submerge and then pop up in some hidden grotto in the Caribbean or off the coast of Chile at your friendly neighborhood pirate chop-shop.
Removing the ship's crew (#2) seems relatively easy, if you have been able to infiltrate some agent or toxin or somesuch. Anything that eats oxygen is bueno, esp fire or some quick-acting oxidation reaction (I suppose). Fire spirits probably would work really well. If you do this underwater, they're unlikely to be able to get a distress call out, too... unless they have a rigger send a drone to the surface with an SOS -- hopefully your action would be swift enough to prevent or intercept that.
It seems to me like the hardest part of this is the first -- finding a sub on the open sea, when it's alone, and force an encounter. Possible ways I can think of:
1) hack their nav computer to display fake results, while actually taking them to where YOU want to meet them. This would be wiz, except that I bet any sub worth its displacement would have a navcomputer that's not on the Matrix. So, that's reaaaally hard to do without actually having been on the ship already. Maybe a run while it's in port or drydock to do this. Would require some highly specialized knowledge and skills not to mention a good decker.
2) subvert one of their riggers to send periodic reports to you via seafaring drone (surface, blip a signal to your favourite data drop, then self destruct or somesuch). This sounds easy, when you consider replacing the rigger with your own stand-in ... except, I suspect that any rigger team (as ships probably have more than one working together) would notice that the New (Fake Old) Guy didn't have the same character in his workings of drones -- much as a decker might recognize another decker not jsut by icon, but by the way he manipulates code or approaches a task. So, you probably need to replace ALL the riggers, or none at all. Note that the more people you replace, the more likely you need to replace everyone.
3) Replace the sonar guys with a stooges, and just have someone follow the ship (while he neglects to say anything)... I think, though, that the sonar guy is probably one of the riggers, so see #2. This makes it easier though for you to have a second sub creep up on an intercept, though! Riggers could also do things like shut down the air scrubbers, or something ...
4) put a "limpet mine" (TW2002 reference! yay!) on the thing, and have it periodicaly release a little floating drone to say "here I am!" in much the same way that the subverted rigger might -- this seems better, in fact, since it's outside the ship and crew's knowledge. This would tell you where it WAS (or was heading), but couldn't really force the ship to surface. So, you probably have to combine this with the crew-incapacitating-solution to render the ship dead in the water (or just heading in a predictable manner), and then sneak in with another sub and ferret in your own crew. (like the sub to sub rendezvous in Red October, I imagine.)
. . .
Of course, Dim Sum wanted something to attack a land target -- not such a good match with the submarine. Maybe the best way to get such a craft (capable of attacking a land target) is to BUY one on the shadow market. It's probably cheaper than funding a theft operation, and is more likely to succeed. That makes it more appetizing to the bean counters, too.
Or, rather than spending your hard earned nuyen on a ship, why not make a run into the manufacturer's host, and fake an order to a fake buyer (complete with datatrails to make the buyer's ID credible ...) Then again, that might be precisely how the shadow market DOES it ... IMO, the shadow market is a big "don't ask, don't tell" -- I don't care if they faked the order, or stole it, or built it themselves, as long as it does what I need.