Both places are correct but you’re mistranslating the number of food. Don’t put a plural when you don’t need it. Food is singular, let it stay and translate by :

Pourtant, il y avait de la nourriture ?

Or :

Il avait de la nourriture pourtant ?

The place where you put it will depend. If the sentence is within a conversation, the first translation is a direct opposition to the predecessing sentence. If the previous speaker said that the last wedding he went to was horrible, the first translation will oppose his argument to yours, the food. The second translation will be more polite.

Note that pourtant is widely used in the familiar language, but a more academic word would be cependant.

If you want to go further, you’ll have to invert the verb and the subject :

Y avait-il de la nourriture cependant?

That last sentence is better in the academic way but less used in familiar language.

Contrarily to @Dranna, I wouldn’t put "pourtant" at the end of a sentence like this. The adverb is most often placed just after the verb. It can be placed at the beginning or the end of the phrase, but then it should be separated with a ",".

Il y avait pourtant de la nourriture.

Il y avait de la nourriture, pourtant.

Pourtant, il y avait de la nourriture.

Note that this construction is for an affirmative sentence. You can make it an interrogation with a question mark and a change of intonation.

Il y avait de la nourriture, pourtant ?

but normally you should have an inversion when you build a interrogative sentence (note that in this case the sentence is also negative).

N’y avait-il pourtant pas de nourriture ?

If order to give the same impression as in English, I would suggest

Il y avait de la nourriture, non ?

Last remark : IMHO, "pourtant" is closer to the meaning of "(al)though" and "cependant" is closer to "however". "Pourtant" is not necessarily more familiar than "cependant".

To add up to other answers, another possibility that I would use is

Cela dit, il y avait de la nourriture.

which can be translated literally as “That being said, there was food”, so it tones potential, previous criticism.
In spoken language, one could also use

Il y avait de la nourriture, cela dit.

which is sloppy phrasing, but might match the original sentence better.