If one of the couple is still alive but the other is not, then it's awkward to just use are or were. Either way would be misleading, and you'd have to follow with some kind of retraction.
Both the Professor and his wife are great scientists, although he died last year.
Both the Professor and his wife were great scientists, although she is still alive.
You see? Awkward.
Instead you ought to rephrase the sentence. One way to do this is to talk about their reputation rather than their existence. It's fine to say what their reputation currently is, even though one or both might be dead.
Both the Professor (who passed away last year) and his wife are considered to be great scientists.
Another way is to avoid the verb entirely and focus instead on their accomplishments:
The Professor and his wife, both great scientists, published their latest groundbreaking research last year, a few short weeks before he died of complications from a long illness.
Unless otherwise stated, we can assume the Professor's wife is still alive.
(Edit) As DonQuiKon's comment points out, you can use the perfect tense considered to have been for past events, but this is more complicated than you might think. The perfect tense implies a relationship between two events in time, and you would not use it unless you wanted to suggest something changed.
For example, suppose you write:
The Professor and his wife are considered to have been great scientists.
This tells us very little. What has changed? Maybe they died? Maybe they are no longer considered great scientists? Without further information, we don't know.
Meanwhile the infinitive works fine for both the living and the dead:
Shakespeare is considered to be the most significant writer of English literature.
The man may have died 400 years ago, but his reputation lives on.