She (sorry about saying he) will be fine with proper treatment. You caught it early, and you've posted in the right place! There are many people here willing to help, so I'm sure you'll get more responses and advice.
Have you set up a quarantine tank before? If not, I can give you some pointers.
Is there a filter in the 3 gallon? If so, thats good. If possible add some of the bio media from the poor things original tank to the small filter in the 3 gallon. (You can just snip off a corner of the bio in the original tank with scissors and put it in the filter. Just shove it down there, any little bit will do.) Another thing to help with stress from a quicky quarantine is to grab a handful of gravel from the original tank and put it in a mesh bag or old, washed panty hose. You can even use one of those thin, silky dress socks. Add the gravel to the bag and tie the end shut. put the bag in the 3 gallon. THis will help with some good bacteria needed to reduce stress and keep levels stable. (Of course, 60-70%
DAILY water changes will also be needed to reduce ammonia build up from waste in the un-cycled 3 gallon).
I never have substrate in my quarantine tanks. Substrate can harbor infection and disease... it just keeps a more sterile environment in the QT tank.
You caught this early, so if you have to net the fishy and remove substrate or just now add a bag of her original substrate, you should be fine.
Here is a quote from another thread where someone needed QT help... I dont think your case is this drastic, as I've dealt with it and never have lost a fish from pop-eye- the thread this is from involves a shark that is MUCH larger than your precious girl.... so just use the info you need.
Okay, Hospital Tank instructions, as requested!!!
1: If you have a filter for the hospital tank you need to add bio media from the original tank to the new one. (You can either cut a piece of the sponge original sponge and put it in the new one or if you use a canister you can take some of the little bio wheels and put them in the new filter.)
2: You need to gather some of the rocks (I would say Softball size amount) and put them in a mesh bag. If you dont have a mesh bag you can use the foot from pantyhose or a thin dress sock. Tie a knot at the end so they dont fall out. Place the bag of rocks directly in the tank.
3: Take water from the ORIGINAL tank and put it in the Hospital tank. (Fill the new tank 50-60% with the water your shark is currently in)
4: Dechlorinate fresh water and add it to the new tank.
5: Set the heater at 75 degrees and place your shark in the tank with as little stress imposed upon him as possible. (would be best to set the tanks up close to one another so he doesnt have to make a long trip from room to room.)
6: Leave him alone. I would fast him (dont feed him) for 12 hours.
7: Tomorrow afternoon, feed him, let him eat as much as he will, and update us on how he is eating- this is a something we need to know in order to help you as the healing process goes on.
8: After feeding, change 70-80% of his water, again, dechorinating the new water being added. Repeat this priocesses DAILY.
9: Pay attention to his waste. If his poo seems white or stringly, let us know. You may also want to vary his diet as allowed, feed him veggies, and minimize protines. Viatmines are just as good for fish as they are for us.
****I MUST stress that DAILY waterchanges of 60-70% will be the best medicine. Dont even miss 1 day. Just to the water changes DAILY and you should be fine.
****Post if she improves, as I'd LOVE the good news, but also post if the wound worsens or she looses her appetite or if poo looks white and stringy.
Glad all is well!