Néhány alma is the subject of the sentence (which could also be translated as, "Some apples are here," to make that a little more clear). It is not the object of any action that would require the accusative ending. Compare...

Van itt néhány alma (there are some apples here or "some apples are here"; nominative)

Tedd le az almát (put down the apple; accusative, the apple is the thing that is to be put down)

Az alma János előtt van. (The apple is in front of János: apple is the subject)

János megeszi az almát. (János eats the apple: apple is the object which is being eaten)

Hol van az alma? (Where is the apple? Subject)

Elfelejtettem az almát (I forgot the apple. Object.)

Also van isn't a 'proper' verb, the accusative case can't be used with it.

Hungarian uses the singular form of nouns if they are modified by a number or most other quantity words, including néhány (some) and sok (many). The verb will match the singular form of the noun. So for example

Van itt néhány alma. (There are some apples here - but alma is singular, and we use van with it)

Van itt hat alma. (There are six apples here - but alma is still singular, and we use van)

Van itt sok alma. (There are a lot of apples here.)

but

Vannak itt almák. (There are apples here - plural apples, plural verb.)

Since numerals already show that we're talking about more than one object, it's unnecessary to use the plural form of the noun (according to Hungarian logic). :)