If it's not against any applicable property disposal rules, I'd have the agency sell them directly by auctioning them individually on GunBroker.com since that'll get them the most money.
It may be a requirement to give public notice of the property auction(s).
Our state has an exception for property traded to a gun dealer, but the agency won't get as much value going that route.
(It does not require any public notice however.)
Any SOT purchasing them will need to provide a LE demo letter (from another agency) for you to forward to ATF along with the Form 5.
If the agency trades them through a dealer, normally they'll be paid upfront (or receive "store credit") and the guns will stay with the agency. As new buyers are found (by the dealer) the individual F5's get submitted (with the trade-in dealer acting as an intermediary) until they're all gone. Might take months. Normally they do not transfer in one batch to the dealer the agency trades with. Because of an ATF limitation on transfers, most SOT buyers can only receive a maximum of 2. There's no quantity limitation for a government transferee.
The CLEO (or his designee) must sign each F5 and they cannot be done in eForms unfortunately, but they can be emailed as a PDF.