As far as I'm able to find, there isn't anywhere in the game that directly informs you on what variety an individual is. Feel free to comment if you've found a way to see it stated explicitly. The exception would be that if you've only ever encountered 1 Pumpkaboo, you can check which entry got filled in the Pokedex, but that won't work if you've already seen multiple.
I found an easy way to tell, however. In the summary screen, all Pumpkaboo of a particular variety look the same, regardless of their size classification. I took pictures of all 4 varieties as a reference:

As I noted in the question, Alpha Pumpkaboo and Alpha Gourgeists are set to always come with a Plus move that's normally only learnable through TM. I will note these as well:
- Small Variety Pumpkaboo - Psychic
- Average Variety Pumpkaboo - Flamethrower
- Large Variety Pumpkaboo - Dark Pulse
- Jumbo Variety Pumpkaboo - Rock Slide
- Small Variety Gourgeist - Sludge Bomb
- Average Variety Gourgeist - Fire Blast
- Large Variety Gourgeist - Shadow Claw
- Jumbo Variety Gourgeist - Giga Impact
Jumbo Variety has a unique cry, and Alphas of any variety have a separate unique cry.
By the way, here are the Pumpkaboo spawn rates for Wild Zone 15:
- 5% Small Variety (Daytime)
- 45% Average Variety (Daytime)
- 45% Large Variety (Nighttime)
- 5% Jumbo Variety (Nighttime)!