Send a letter, by all means, especially, if you have something nice to say about the niftar. When I was an aveil, I treasured the letters I got, especially, those that had something to say about a chesed, that was done, by the niftar. It meant so much, and I have those letters to read as a keepsake.
During shiva, it is hard to talk on the phone, especially, when you have people around and they can not give you their full attention.