When I took my wife to Hawaii in 1980 (from Seattle), either there was no direct Seattle to Hawaii flight or there was only one that got there too late to get to the outer islands. I am not a particular go to Hawaii fan but we have a number of friends who do; and a client who has a division of his business there; the routing people talk about is through San Francisco. In the early 1960's, it would not surprise me that San Francisco was the only route.
So yes, Seattle would be out of the way in airline routing to Boston. Plus which the Boston fairy tale has a problem with the fact that Obama Sr. wasn't there until a year later and it isn't likely he was there much earlier because he was also considering an alternative education grant that would have been sufficient to pay for taking his wife and son.
Airlines were subject to two major disabilities in the 1960s when it came to the Pacific.
First of all, the Pacific is really big and planes then commonly used could barely make trips to Hawaii from San Fran and Tokyo. The 747 was put into service in 1970. The 737 in 1968. The 727 in 1963. The 707 saw its first flight in 1957.
The other disability was government regulation. Without an established rate no airplane at all could fly on a commercial route.
The new, big jets being planned and built by Boeing forced the issue of establishing rates for passengers, cargo, baggage, express and mail on routes that'd never before existed.
1961 was not really a good year to look for a cheap trip to Africa Fur Shur.