If Doctor Eckelburg were God, surely it would make more sense for him to be frowningat Tom rather than 'with' him, because as we know Tom is waiting for his mistress, Myrtle, and from a Christian standpoint is committing the sin of lust. Yet, the use of the word 'with' corroborates the earlier point about Doctor Eckelburg's morallymyopic eyes. This implies that instead of being a 'God' it is a morallycompromised 'god', who, while looking over much of man'sdomain, also overlooks much of man's sins, highlighting the theme of moraldecay.
"The eyes are not here" - this line could imply that there is no god or higher power watching over us, but it can also mean that if there was one he wouldn't care anyway