Six people were in the boat when it overturned in Loch Gairloch. A man and a girl, 10, managed to swim to shore and alert the coastguard at 16:15 BST.
A helicopter and lifeboats launched a search and found the two boys, aged five and three, and a girl of five. The girl remains in a serious condition.
The search for the missing man, aged 34, has been called off for the night.
A coastguard helicopter and lifeboats from Portree, Gairloch and Loch Ewe were involved in pulling the children from the water.
The three rescued children were taken to Raigmore hospital in Inverness and Broadford Hospital in Skye.
Northern Constabulary confirmed the boys' deaths.
The man and girl who swam to shore were uninjured.
Searches were carried out in the water near the Big Sands caravan park.
Local boats and onshore coastguard teams assisted with the rescue efforts. They plan to search again in the morning.
Northern Constabulary said the group were in a Canadian canoe, a narrow boat designed to carry numerous passengers.