Full disclosure, I only have the Vaporfly 4% and the Alphafly Next%. My response assumes that the Vaporfly 4% is at least comparable in some small way to the Vaporfly Next%2
In the world of crazy super shoes, it probably needs to be said these are both competent and capable shoes. I don't think that there is a wrong answer here but, as Kaleb mentioned above, personal preference will be the deciding factor. For me, the Vaporfly just feels springier under foot. I don't know if is the air pods or what, but the Alphafly doesn't seem to have the same comical bounce (that I love) from the Vaporflys. Add to this that while the Alphafly doesn't feel unstable, it also doesn't feel supremely confident when at top speed for me.
I plan to happily run my Alphaflys into shoe retirement but my next racing shoe will definitely be a pair of Vaporflys.