There were many U-boats still active, yes. They still had means of communicating, the same way they had during the war: via radio.

Let's look at one in particular that has been scrutinized very closely, the U-234. In May 1945 they were in the Atlantic, en route to Japan (they were delivering technical materiel to the Japanese, which is why they have been scrutinized). They heard a fragment of UK radio on May 4th that said Hitler was dead. They surfaced on May 10th and received a transmission from Admiral Dönitz, who had taken control of Germany. Dönitz's order said that the war was over and that the submarines should submit to Allied forces. The commander of the U-234 contacted another submarine to verify they had the same message. The U-234's captain said they were going to go to Canada to surrender, but actually went to Portsmouth in the United States (they thought the Americans would give them easier treatment than the UK or Canadians). He surrendered his ship there, was interrogated over its contents and mission, and then he was eventually sent back to Germany. The ship was kept by the Americans and was eventually scuttled, several years later.

The U-234 is discussed at length in Joseph Scalia, Germany's Last Mission to Japan: The Failed Voyage of the U-234 (2000). This is what the messages sent sort of looked like — this is a US decrypt of a radio messages being sent to subs, trying to coordinate their surrender. (That one is from the National Archives; I was helping some people do some research on the U-234 and a few other similar subs some time back. That particular one is for German subs that were in Japanese ports.)