In general, you should include both parents’ income and assets in net price calculator runs for schools that use non-custodial parent information for financial aid. If you need the waiver for the school to be affordable, you should treat the school as a super-reach, since getting the waiver is unlikely.
Looks like the OP’s main barrier to many “good financial aid” schools is the non custodial parent requirement. So many such schools are automatically super reach for the OP.
You may want to ask your counselor if she has known any students with similar non-custodial parent situations that you have who have applied for non-custodial parent waivers, and which colleges granted or did not grant the waivers.
If any specific colleges appear to be more likely to grant the waivers, these may be the ones that have a somewhat better chance of success for you than those with a history of not granting the waivers. On the other hand, colleges with a history of consistently denying the waivers are likely to be a waste of effort and money to apply to if you need the waivers to afford them.