I am traveingl with a number of small children and wanted to avoid a 3+ hour tour and just buy the" skip the line" tickets ahead of time. Is that possible as I couldn't find a link on the Vatican website to do that?
When you buy tickets you have to select an entry time.
The line you skip is the very long one for people that show up without a ticket.
This is the official site
http://www.museivaticani.va/content/museivaticani/en/visita-i-musei/scegli-la-visita/musei-e-collezioni.html
What ages are the "small children"
Here is the ticket site. All you want is the admission.
https://biglietteriamusei.vatican.va/musei/tickets/do
This audio guide may help to engage them.
Just a thought - since you say you have a number of small children - is going to the museum even worth the time / hassle / expense? Only you know. For the Basilica itself, there is free admission and no tickets are needed. Enjoy your trip!
Current reports indicate that the Vatican Museums are massively crowded at most times. I'm not sure it's a good idea to take small children there; they may not be able to see much of anything. There are ways to get you inside before the public opening time, but they all cost extra. I think there's an early-morning option on the Vatican website. Commercial early-access tours are more expensive than what the Vatican offers, I think.
If your time in Rome includes a Friday, look at the night tours.
https://biglietteriamusei.vatican.va/musei/tickets/do?action=booking&codiceTipoVisita=78&step=2