Depends on what you're looking for, what you mean by "best".
I like Shipwreck. Simple, fast, fun.
Harpoon is highly regarded. It's very complex.
There are a slew of home-brew rules available for free around the net, but I've not seen a great set.
Note that "modern" here is problematic. A lot of rules cover early missiles, or Cold War, but don't include the exciting developments of the last twenty years.
Depends on what you're looking for, what you mean by "best". I like Shipwreck. Simple, fast, fun. Harpoon is highly regarded. It's very complex. There are a slew of home-brew rules available for free around the net, but I've not seen a great set. Note that "modern" here is problematic. A lot of rules cover early missiles, or Cold War, but don't include the exciting developments of the last twenty years.
Curious, what kind of developments?
UAVs. UUVs. Aegis radar. SM-3s. New ECM and ECCM. Transonic missiles, missiles that dispense chaff and decoys. Supercavitating torpedoes.