1 kg (about 2.2 lbs) of Anti-matter (and supporting matter and "mixing" hardware to bring the anti-matter into contact with the matter) = 20Megaton (rough), assuming 50% efficiency.
Note: the US "B41" type 25 MT bomb, the biggest the US ever produced, was about 10,670 lbs.
The USSR had the "Tsar Bomb" that was tested at 50 MT, the biggest man-made explosion ever, and had a theoretical max of 100MT yield and was about 27 tons in weight.
Win to Trek.
Also most nukes in space "waste" a lot of their energy radiating in all directions, if you don't have a "contact hit" only a fraction of the energy needs to be absorbed by the ships armor. Shields can also "deflect" energy before it gets to the hull if they are "tuned" to whatever form that energy is in (Or so I assume, we can do it with some EM type energy in a few frequencies with today's tech).
In addition:
In the Trek Universe the computers are fully integrated. In BSG they are not (with good in-universe reasons). That means that reaction times, fire-control solutions, and other vital calculations for fighting are going to be MUCH faster on the trek-based ships. Even with good computers in the BSG ships, they have human "links" to actually fire the weapons and do other functions, and this will slow the systems down by factors of thousands compared with a full-on Trek-style computer system.
In WWII, during the Second (Naval) battle of Guadalcanal the US and Japanese battleships had a pretty even parity in weapons and armor. However, the US had Radar, and as a result could hit the Japanese ships before the Japanese could even range on the US (although they did, eventually, but they lost). The lesson here: you can't hit what you can't see, and in space at the ranges you might be at, reaction time and calculations (like areas of probability of where an opponent might be when a sub-light weapon reaches it) are going to be vital. Slugging it out at visual range is a TV artifact (um...yeah...I know...it's a couple of TV shows...).