I have never played a wing commander game, and I was browsing through GOG and came through these two games. What would you guys suggest is a better purchase (for someone with no wing commander experience), Wing Commander 3 or Wing commander 4?

well in all honesty both are great games but you really should play the full series or parts of the plot wont make sense. so I would suggest getting the bundles wing commander 1+2 first.

That being said 3 is not the worst place to start because many of the characters in 4 are also in 3 and it does in some sense make a somewhat clean break from 2 with by starting out with destruction of the Concordia. but there are parts of the plot you wont completely get and interactions with some of the characters that have to do with their histories that are useful to understand for the interactive movie components. keep in mind that the decisions made in the movie components changes how the other pilots perform in their flights in latter missions.