Well Thor can easily absorb Vision's forehead blast no problem, and I don't know how long Vision can maintain his intangibility, but there's no level of density increase he can obtain that Thor can't still send flying.
Well Thor can just phase to match Vision, or phase himself to another dimension and attack the Vision from there.
Thor would wipe out the Vision in a few minutes.
__________________ Among the tales of sorrow and of ruin that come down to us from the darkness of those days there are yet some in which amid weeping there is joy and under the shadow of death light that endures.
J.R.R. Tolkien, "Of Beren and Luthien" from the Silmarilion
I've always thought he should be able to, considering that he can create higher dimensional worm holes where ever he wants. Phantom Girl in the Legion of super heroes is able to phase/become intangible, as her body exists in two separate Dimensions at the same time. I suppose the same physics could be applied to Thor.
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'The only sock around here is on my 'japseye'. - Yahman