Yes, I think if the noise is a result of the gear mesh new gears could be noisy too, unless you had a new original set, as I hope they would have been quiet when new. A worn bore might be easily cured with a new gear, or good used gear.
Trying to isolate a gear noise is not easy....I used a mechanics stethoscope and checked it over while it was running with the drive shaft removed and finally convinced myself it was the transfer case. I was prepared to rebuild it again and change all the gears, but the easier intermediate gear swap did the trick....