The bus will be a quicker ride. After arriving at the bus area at DHS, there is about a 10 minute walk, depending on which bus slot is used (don't remember), to get to security. Buses run every 20 minutes.
The FriendShip boat from the International Gateway runs about every 15 minutes, and the ride makes three intermediate stops on the way to DHS. Actual travel time is about 35 minutes from Epcot to the dock at DHS. From the dock, it's only about a 5 minute walk to security.
From the MX pavillion at EP, I would think that the walk to either the bus or boat is about the same distance.
With either option, I would allow one hour, which includes a possible 15-20 minute wait for a bus or boat. There is no issue, right now, with any Skyliner construction, which is near the IG. If the weather is rainy or very sunny/hot, I would choose the boat, as there is some overhead shelter. The boats will not operate if there is lightning in the area.
From your location at EP, I don't think you would save much time walking to DHS, and if the weather is not the best, you could be caught on the walking path, without shelter.