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Is a hit and run attack a boarding attack? i.e. can a chaos ship with mark of nurgle be targeted by a hit and run attack (since it cannot be boarded)?

No, a hit and run attack is not a boarding attack. A ship that cannot be boarded, such as a Chaos ship with he Mark of Nurgle is not automatically immune to hit and run attacks.

It's on Page 35 in the rulebook, under the Hit-and-Run Attacks section. It's kind of funny, because a Chaos ship with the Mark of Nurgle is specifically mentioned in the example used - I didn't realize that until I looked it up. It's also the 4th page on the Advanced Rules PDF piece of the living rulebook.