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The easiest place to start would probably be Restall's Seven Myths of the Spanish Conquest. He didn't set out to specifically counter Diamond alone, but rather to combat the misconceptions and pitfalls that popular history, and Diamond, fall into when discussing contact in the New World. This is a fast, fascinating read, and a wonderful place to start your journey.
Please let us know if you are interested in a specific place, time, or theme. Diamond's book is wide-ranging and no single volume will be able to tackle all of his theses in one brush, but we can make targeted recommendations based on your interests.
It’s not exactly the same theme, but 1491 by Charles C. Mann covers a lot of the new research that makes Guns, Germs, and Steel a bit outdated. It’s about what North and South America were like before colonization. Mann argues that Native civilizations were actually much more population-dense and “advanced” than they are often portrayed — the fact that early colonists perceived so much of the land as “empty” is probably due to the killer wave of smallpox that preceded them, decimating these societies. In other words, the lack of guns and steel didn’t actually hold Native societies back as much as Diamond claimed, though germs were still a problem.
“nobody has yet given me a viable antithesis or coherent alternatives”
You have basically hit a perennial problem with environmental determinism, the tradition in which I would place Diamond’s work.
Even if you fundamentally disagree with it, determinism seems to provide rational explanations to why things are the way they are: it gives us nice, logical answers. X happened because of Y because of Z. This quality makes it both appealing to some and very problematic to others.
The contrary view, possibilism, which also has attractive qualities, is inherently uncertain. Possibilism makes no claim to have all the answers because at it’s core there must be an element of uncertainty to history!
If someone tells you the book is outdated - they are right in a way that the basic thesis is very old. Environmental determinism in some form is at least as old as geography itself, and divided opinion over it is rooted within the deeper philosophical question of the existence of free will (which I can’t see being resolved anytime soon).
For the same reason, it cannot be fully discredited: the argument is not going away, people will probably make arguments along the lines of Guns, Germs and Steel’s for centuries to come.