Most people use these, but they have to still be modified slightly (from digikey and mouser):
https://www.digikey.com/product-detail/en/S8421-45R/952-1737-6-ND/3131076
http://www.mouser.com/ProductDetail/Harwin/S8421-45R/?qs=Qom7kyPojXY6z0Gmx3V3RQ==
Nothing fits exactly, but these are essentially the ones people use the most since they are low enough in profile to fit between the cart and the PCB. There is a youtube video out there on how to modify them correctly (really mostly just bending the clips and trimming a bit):
https://www.youtube.com/watch?v=uYFXNEH_vvk
They might need some more changes to fit on all the various carts out there (due to other chips/items that might be around the battery area), but for the most part, these are the smallest ones out there that people use for this job.
Edit: Also, if you don't want to lose your game saves while you install the battery holder, I recommend attaching a backup battery in parallel to the existing battery on the cart (get something like a 2xAA battery holder which has 6-10 inch wires, and then use a multi-meter and your eyes to follow the traces on the cart which connect to the existing battery to find 2 other contacts that you can use to connect the wires from the 2xAA holder).