What tone for retroflex r?
In pinyin erhua is usually written with a natural tone:

r

哪儿, like you mentioned above, for example is written:

nǎr

Erhua is tacked on to the end of the pinyin and the tone is in the usual place for the preceding character.
An easier way to see this is probably for a word like 瓶儿. 瓶儿 is written:

píngr

The erhua is not merged into the pinyin (like you may see in some topolectical Romanizations) but just placed at the end somewhat unsightly. This is because the whole word is read as a whole and not in parts.