Since 15/7/2016 foreigners can enter Co To island without a permit: Travel to Co To Island from Cai Rong?
There are some official news in Vietnamese but unfortunately none in English
As per Vietnamese regulations, foreigners coming to borderside areas must register with local police.
Due to the military presence on the island a permit is required to stay on the island. The permit needs to be acquired in Ha Long city beforehand. If you arrive without a permit you will either be expected to pay a fine or be sent back to the mainland. (This information does not apply to Vietnamese nationals)
Co To is also a border district island so you need to register before coming. Those documentations are often done by tourist companies. However in recent years many foreigners who travel on their own didn't know about the regulation so they bought boat tickets directly to the island without registering first and were not allowed to stay.
If you're working in Vietnam, things are much easier. If not, there are some tourist agencies that will work out the permit for you. You can read some information here Forbiden island: Three documents a foreigner needs for a vacation in Co To
However AFAIK it's possible to get an on-arrival permit because since 10/10/2014 a special group was formed at Van Don port to give permits directly to foreign travelers who didn't have one (source: Vietnamese only).
But if you're visiting Ha Long then I think you should have time to get the permit first. That would avoid many hassle. It wouldn't take much time, because only a few foreigners come to the island each year. Information from Quang Ninh province says that in the first 9 months of 2014 there are only 400 foreigners enter Co To per total 100000 (again Vietnamese only). You can also book a hotel on Co To first and have them get the permit for you
Another nearby island, Co To Con (small Co To), can be visited without any permission. Unfortunately currently there's no direct boat to Co To Con. You need to travel to Co To and then transit to Co To Con