RPG

Best for what purpose?

There's no universal "best" because different people want different things from their spaceship combat games. Myself I like quick resolution and simple record-keeping so I always kit-bashed something with the old Starfire wargame to warp it to the RPG setting. If you're not into kit-bashing, though, that's not going to be "best" for you.

For spaceship combat that was tense as a suspension bridge truss, the one that was made for Traveller:2300/2300AD was really, really good, but it was very much glued with cyanoacrylate to the setting.

The original Book 5 for Traveller had a ship combat system that was very much about capital ship combat in large fleets (and could barely scale down to smaller conflicts like individual ships). It was "perfect" for that kind of thing, but again was glued to the setting (albeit more with some contact cement rather than superglue).

The Jovian Chronicles (game, not Mekton Zeta supplement) space combat system was rather nifty and came with a nifty spaceship design system (albeit one that had a "dreaded" cube root in the construction rules that made people panic). And while it was made for a setting, it was much easier to kit-bash for other settings.

For more generic games, if you want the scope and glory of space opera, the game, well, Space Opera is hard to beat. It's an old design, so filled to the brim with odd, crunchy, ornate bits, but it was a whole lot of fun when I played it. Just ... be ready to fill out a lot of papers and roll a lot of dice many, many times.