This was way before the repurcussions of Marbury vs Madison which is where the court openly stated that it had the ability for judicial review. Hamilton was all for this if you read the federalist papers (also some people argue that the Court practiced it, but that that case was where they put it into writing), but the Supreme Court of Hamilton's days was far weaker no matter how you look at it.
As for how powerful the Judicial branch is it really comes down to the individual courts. Some of them have been tremendously powerful (ie the Marshal, Warren courts being the most famous in expanding the courts power) while others did little for decades. People tend to describe the Courts by their chief justice as they are the most prominent members of the court, even if they are the dissenting person every ruling.
Andrew Jackson was a populist president and it's generally agreed that if the population wants something by a sizable majority then the state will either carry out their will or collapse (this is massively generalized/simplified). The courts ruling against Jackson was powerless because the vast majority of the country backed Jackson's position - Jackson would have had to position troops to prevent the populace from doing what his troops did instead, and as he himself did not support the ruling would have been against that.
Anyways, the justices are probably the most powerful individual members in the government and the freest to express their actual opinions due to the lifetime appointment. The President is more powerful during wartime than the Court as a whole (and the president tends to have more influence during wartime with the Court) but I would say the current court is more powerful than the presidency when not at war
The executive branch itself is where it gets tricky because there's no way that the president can know every single member of his cabinet perfectly. A president with a weak, corrupt or ineffectual cabinet is going to be less powerful than one with a good cabinet regardless of their personal political prowess (though appointing a corrupt cabinet is a good sign that they don't have any political prowess - see Grant and other failed presidencies).
The legislative branch would be the most powerful if they worked together but that rarely happens. The legislative branch can make anything constitutional with sufficient votes. They can also give the president more power by declaring war.
The Dredd Scott decision was criticized by Lincoln for reasons of removing power from the hands of the people. It was a ruling that occurred mere decades after Jackson's decision (Lincoln made these comments well before becoming president).