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Since manipulation of the brain is prohibited and illegal modifications are assumed to be reliably caught, the obvious way to check someone's identity with biometry would be by checking their brain.

One thing I could imagine is that there are recognisable patterns in the EEG that allow identification. These could be either patterns that are permanently found, or patterns that are the result of specific stimulation.

Therefore the biometric identification process could involve using an EEG cap, and for example watching the response of the brain to specific sound patterns played over your headphones.

Obviously the “something you know” and “something you have” components would not be affected by genetic manipulation, however I could imagine that the “something you know” component could take advantage of the EEG cap as well, by reading directly from your mind if you recognise certain things presented to you. Since that way you don't provide any visible evidence of what you know and what not, that method would be reasonably secure from physical eavesdropping.