Ms McGuinness is currently vice-president of the European Parliament.
She told RTÉ's This Week programme that it was a decision for Government and that nobody from Government had been in contact with her over the position.
When asked if she would be happy for her name to go forward along with Minister for Foreign Affairs Simon Coveney, Ms McGuinness said she would have no hesitation.
She said Ireland has been through a "difficult patch" as the controversy over Mr Hogan's attendance at the Golfgate event made headlines at home and abroad.
European Commission President Ursula von der Leyen has asked the Government for one male and one female candidate to fill the role left vacant after Mr Hogan's resignation.
It's not good for us, it's an uncomfortable position.
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Ms von der Leyen also cast doubt over whether Ireland will retain the EU trade portfolio. Ms McGuinness said she hopes that Ireland can move on from the controversy over the Oireachtas Golf Society event, and focus on important European issues again.
"I think it's very clear that when any member state is at the centre of a difficult crisis or controversy, it lasts over a number of days," she said.
"It's not good for us, it's an uncomfortable position ... and I think what we will be measured by now will be our ability to recover, to get on with the business at hand, and to meet the requests of Commissioner von der Leyen."
Ms McGuinness said that Taoiseach Micheál Martin handled the situation well. She also said Ireland's reputation within the EU had not been irrevocably damaged.
"This is about somebody who is committed to Europe, and I think we have forgotten that here in Ireland. We have focused on Irish interests as if they're exclusive and different from European.
"Whoever gets this position man or woman, will be required to be a European Commissioner, clearly with an Irish background, but not only batting for Ireland."
Ms McGuinness said it would be "unwise" if the Government decided to only put forward one candidate.
