Nomads have no doubt a lot going on for them. They are physically stronger, can attack at a time of their choosing and can run away to safety. The only things working for city people are:
City Walls
By and large thats the historical reason in our world why nomads aren't able to conquer most of the cities. In absence of gunpowder city walls rarely failed to protect cities.
In the 1600s setting your story has, gunpowder isn't yet reliable enough. Also, it cannot be made in large enough number. More importantly metallurgy isn't developed to the extent of having sufficient number of reliable (that don't explode on itself) gun barrels.
Terrain:
Cities' locations are wisely chosen. They have to be near a water source ofcourse and the water source in almost all cases also acts as a transport channel. A sea port or a river port is usually expanded into a city.
By having one reliable channel open for transportation the other sides of the city can be in tough, barely passable terrain. The way to city can be rocky, marshy, foresty etc with extra points for having poisonous insects and reptiles (including stingy bees).
The terrain can also be muddy or tundra in summer months which is the only time a nomadic tribe can make a raid. You see those nomads have a big weakness, they don't store grains and loots cannot be reliable. Their only edible storage is in form of animals and those animals are continuous food consumers themselves. The food that those animals consume is ofcourse grass and leaves which are hard to find except in summer.
A city in middle of a desert or any non food growing area would be almost impossible for any nomadic group to attack.
Technology and Industry:
Cities are not just centers of trade. They are also centers of knowledge. Technology would be developed in a city and spread from there. Thats why city people will always have an upperhand in technology (unless the nomads have already captured another larger or more advanced city and is able to utilize its technology).
Cities will always have industry. They can apply the technology developed in industry to produce large number of weapons. Nomads will always lack in numbers in these things.
Cities can store a large number of weapons and ammunition too. Nomads being on move will have disadvantage there too.
Large Population:
Cities will always have relatively large number of people no matter which century you are in after adoption of agriculture. It means though city people are softer than nomads they can very well cover this with their large number. You see Hannibal never even attacked Rome. Rome was a large city with population in hundreds of thousands in BC!
Wealth:
Cities are always richer, a lot richer than neighbouring areas even if the neighbouring areas are settled villages. Therefore, cities can always pay nomadic tribes to leave them alone, byzantinian style.
The money paid to nomads would be a large sum for them but still a small amount for the city. Nomads in 16th century couldn't even imagine how much rich a city can be.
City Buildings:
Have you ever visited an old city or happens to live in one? Did you notice that almost all streets are narrow and never straight?
Thats mostly by design. It provides protection. Even if a nomadic group or heck any army nomadic, village or city people, entered a city it has to fight street by street, house by house. Each building can act like a small fortress, raining down stones, debris, and even dust on the invaders in those narrow streets. Even if the army is of high number it cannot utilize it because of the narrowness of streets.
The army has to take each building individually and that takes a lot of toll on the invaders. There is no telling where a street lead to or even if it lead to some place or just end up as a blind alley. There is no telling at which turn another street open up at a side with city defenders waiting fully prepared.
If the city buildings are build with stone or bricks it would be near impossible for any invading army in 1600s to blow up or tear them down. The city folks can have water wells inside those buildings and food stored up for months or even years (grains can last for years in storage in edible condition).
Even in 1942 German Army had huge trouble fighting inside Stalingrad and got immensely defeated there. Even today Russian Army try to bypass large cities and industrial centers (themselves cities though smaller ones) because fighting inside a city is a nightmare in all ages.
The only reliable way to conquer a city is through siege. Wait out the time the city people run out of food. But nomads cannot really do sieges because they don't have ships. City people will always trade through water ways in the 1600s setting.