Do you have a pic of the actual xtal? I'm guessing it's not a 61.44 fundamental xtal... most likely a 5th overtone. Just curious whether the xtal is actually specified as a 61.44 MHz 5th overtone xtal, or if they just used a 12.288 MHz in a 5th overtone circuit. 12.288 MHz xtals are readily available.
I'm not confident enough to say they'll be drop in replacements though, so I wouldn't place an order for them specifically. If they don't "just work", you can probably make them work with some minor tweaks to the circuit... but you'll need an oscilloscope, assortment of parts, and some expertise. You could probably make something with a programmable oscillator as well, like the DS1077 or DS1085.
I just looked at the schematics... it looks like the same crystal was used on DK, DK Jr., and DK3 (and probably other Nintendo boards), so maybe you can just find a dead board to scavenge one from as well.