While I feel that Transformers slightly outdoes Spidey, an argument could be made for Spidey's bigger focus on practical effects. For all of TF's positives, there's no practical effects on par with Spidey's fireball or lowering building prop. It should be noted that Transformers also lacks any full 360-degree spins. TF is too fast paced to waste time spinning around but it could be a negative if you really like those moments on Spidey.
Transformers and Spider-Man actually compliment each other extremely well. If you want nonstop fast-paced action that focuses on amazing screens, pick Transformers. If you want a ride that's a bit more methodical in its pacing with an increased focus on practical sets and effects, pick Spidey. TF is a bit more to my personal tastes but both rides are still amazing and neither really devalues the other. I've ridden Spidey numerous times after riding TF and still had a blast. If you like Spidey, you'll love Transformers.
However, Spiderman's improved projections, integrated practical effects, and more universally known characters puts it slightly ahead for me. The anti-gravity sequence is one of the most well-done dark ride effects ever (up there with the Haunted Mansion's ballroom ghosts, Tower of Terror starfield/window effect, and the HPFJ Deamentor effect).
Walt Disney World's Magic Kingdom
Disney's Animal Kingdom
Disney's Hollywood Studios
Disney California Adventure
Universal's Islands of Adventure
Universal Studios Florida
Universal Studios Hollywood