In the summer and fall, bonito are most often encountered as they chase bait on the surface. At this time, it's possible to catch bonito from shore, although it's far from a sure thing. By far, those who fish from a boat have the advantage.
When fishing a surface-feeding school of bonito, the approach is key. Avoid running up to the fish at full speed, which often puts the fish down. Instead, either idle up slowly or try to position the boat ahead of the school by at least several hundred feet and shut off the motor(s), then begin casting to the school as it passes. Be sure to try different retrieves and depths, and don't be afraid to let your lure or fly simply free-fall or dead-drift.
If the school goes down, hang around and wait for it to come back up, or watch for other schools in the area. If you're patient, you may notice that the fish appear at predictable places time after time. In this case, simply anchor in the area and either wait for the fish to pop up or blind-cast. Remember, the fish you see on the surface are only a fraction of what's available below.
If bonito are popping up sporadically and sounding before you can get off a cast, or if they are simply not showing on the surface, trolling can be effective. Trolling works well along rip lines, and allows you to cover the entire length of the rip to find where the fish are holding. Just about any lure used for casting can be trolled for bonito, including flies.
While not widely practiced in the Northeast, fishing live baits in conjunction with chum can be a very effective way to catch bonito. This technique is much more popular in Florida, where it's used to attract Spanish mackerel and little tunny. It works like this: anchor your boat along a channel edge, rip line, inlet or any place bonito have been sighted and there is moderate current. Next, deploy a bag of frozen chum to create an oily slick, then toss out an occasional handful of live baits behind the boat. Once the bonito appear in the chum slick, drift back flies or lures to the feeding fish, trying to match the drift speed of the chum. Every so often, toss out some live baits or small chunks of chum to keep the fish in a feeding mood.