For many rides, you can bring the wheelchair in the queue with you if you'd like, or if the queue isn't wheelchair accessible, the CMs at the entrance will tell you the procedure (for example, they may give you a return time instead if a wheelchair can't go through the queue). You can also choose to leave the wheelchair at the stroller parking area if you'd prefer, and I assume crutches in line would be handled the same way other mobility aids are, which is to leave them with a CM at or just prior to boarding the ride and they will move them to the exit for you if needed (ex. for rides where you enter and exit in different places). Her crutches (or wheelchair if you choose to bring it in line) should be waiting for you when you get off the ride.
The only thing you might want to consider if you sister wants to use both crutches and a wheelchair at different times in the same day is what you will do with the crutches when she is being pushed in the wheelchair. If she has folding crutches that would make things easier, but standard crutches might be a pain if she is trying to hold them while being pushed --- they tend to be awkward to hold and their length means they get in the way fairly easily. You might want to consider whether another member of your party would be able to hold onto them for her while she uses the wheelchair to have a smoother experience.
Feel free to check out the disABILITIES! sub-forum if you have more questions or need more details! I'm less familiar with the DL parks than WDW when it comes to the specifics, but rest assured, as someone who uses a rolling walker in the parks due to chronic illness, Disney has a good system for accomodating mobility needs, and your sister should be able to use whatever type of aid in line she may need.
