Answer: I prefer doing suburi with a bokuto (or bokken). It is simply because it gives me a sense of a sword. In addition, it is a good idea for beginners to use a bokuto too. The reason is the same as above; a sense of a sword.
But in kendo we use a shinai. So it is important to do suburi with a shinai too. Shinai is longer so the balance is different. You have to get used to the shinai you use; otherwise, you feel awkward when you do kendo with that shinai.
Do a suburi with both. In that way, you can still feel the sense of the sword and also get used to the shinai you use.