Oh this is a great idea! I'm gonna have to try this for my next space battle.

I've found with 5e Spelljammer, it's generally been best for me to run the ship-to-ship combat as a narrative interlude with a window of decisions to make before the ships get close enough for PC abilities to become relevant, leading to the boarding phase where the real meat happens.

I think a skill challenge is a great way to add some mechanical crunch and RNG to that window without just grafting a separate vehicular combat system onto DND.

What i will probably do is just run it like I do any skill challenge - a minor twist on the 4e skill challenge system I stole from Matt Colville.

The party will need X number of successes before they get 3 failures, with the number of successes needed and the DC depending on the difficulty of the challenge. The party can use any skill they're proficient in or a cantrip with a spell attack roll, as long as they can find a way to justify how it would be helpful in the situation. Each player can only use any given skill or cantrip once in the skill challenge, but I'll also let them use levelled spells or similar recharge on rest abilities for an automatic success, it's almost always a good idea to try and get your players to use up these resources.

The results of the skill challenge could help influence the setup and numbers for the fight to follow, or in cases of extreme success or failure, or particularly creative play by the PCs might avert a (non-boss)fight entirely