Yes and no.
To be accessible, a person with a disability (specifically a person who uses a mobility device) must be able to enter and use the space in a way that is safe/manageable for them. To me, "accessible but not in the way people would like it to be" would be a ride where, instead of going through the main queue that's themed and part of the experience, you have to get escorted through a back hallway somewhere. Or you can board the attraction BUT have to sit in a specific section that isn't the one you want because that's where the accessible cars are. Anyone with a physical disability can still experience the attraction, but it's not the ideal experience you might choose if you didn't have the mobility aid. If you say that anyone who uses something other than a manual chair must change to the manual chair, then that ceases to be accessible for people whose needs are not met by a manual chair. Pirates is perfectly accessible to my friend with CP because he uses a 'regular' wheelchair; it's inaccessible to me (in my electric-powered chair) unless a CM feels generous and pushes me as I cannot use a manual chair. For someone who has trouble transferring multiple times in a short period, Pirates - and any other ride that requires transferring from personal chair to other-chair and then from other-chair to vehicle - is completely inaccessible. That makes it conditionally-accessible.
The next question becomes, whether that conditional accessibility is permitted or not.
Per the most current version of the ADA (post-2010 amendments), a wheelchair is a wheelchair whether manual, powered, or hybrid. And a wheelchair must be allowed in anywhere that a member of the public can go. "Other types" of mobility aids, which includes scooters and segways and non-wheelchair motorized devices, must be accommodated unless that particular type of device cannot be safely accommodated based on 5 factors. According to the DOJ, those factors must be evaluated based on the device itself, NOT based on stereotypes or assumptions about how a person might operate the device recklessly - in other words, you can't ban scooters from an area because some people don't know how to operate them very well.
So by dividing wheelchairs into manual (permitted) and electric (not permitted), they're not following the law regarding accessibility.
The other question is whether the law applies to Pirates or not. Technically the ADA applies as long as the building has been redone in any material way since 1990, and I don't know to what extent Pirates has been. I suspect it qualifies - and moreover, since the issue is one of policy rather than infrastructure (e.g. you can get there without using stairs, they just won't allow certain types of wheelchairs in there even if that wheelchair can maneuver through the queue), it would most likely be a violation of the law.