Beyond the window was the river, the trees, the sky.
A basic rule of grammar is that a singular subject takes a singular verb, and a plural subject takes a plural verb. Since the subject of this sentence is plural (the river, the trees, the sky), it needs a plural verb. It should read like this:
Beyond the window were the river, the trees, the sky.
There are exceptions to every rule, and many exceptions to this rule. But I don’t believe that any exceptions apply in this case.