They are separate services. Some campgrounds seem to be on both. In some cases, we've found a campsite we like on one, and have been sent to the other when we begin the reservation process. when that happens, we just go to the other to make the reservation/ For whatever reason, most of the sites we've reserved last year and for this season have been on recreation.gov, even the non-NPS ones.
For CO, state parks and some country parks are available through reserveamerica.com. All USFS sites are available through recreation.gov. The interfaces are nearly identical and the visualization of the campgrounds and sites are also nearly identical. For CO, you can search on any CG from either site. However, if you're on RA and want to book USFS, it takes to to Rec.gov. If you're on Rec.gov and want to book state park, it takes you to RA.
Last time I used the government site to reserve I believe there was a difference in the processing fee or in the cancellation process. Whatever it was, it made more sense from a financial standpoint to use the government site so I did. It was two years ago so things may have changed.
Both are run by Active.com and are awful. Do some searching on the scam the run on tricking people into signing up for an Active.com membership during the reservation process that automatically renews on your credit card. I guess recreation.gov is where they list the campgrounds whose government entities they've managed to get into bed with to handle reservations. In the state of Louisiana we have to pay a $6 "reservation fee" to them every time we camp even if we show up and pay at the gate (i.e. we haven't used their online service or their 800 number). Last time I was on an out of state trip I could camp all over Arkansas for under $20 per night with hookups in fantastic parks. In Louisiana I can't camp anywhere with hookups for less than about $27 for a single night by the time everybody gets their piece of the pie. It's only charged on the first night's stay but it still makes me mad especially if I'm just staying for one night and then will be onto the next place.
They both use the same database, I normally use ACoE or NFS, but when I went to make a reservation at a state park I used my id from recreation.gov and it had all my information.