So, the short answer to your question would be that the circumstances of the country at the time of those major waves of immigration were entirely different.

The long answer:

The first major wave of German immigration to the what would become the United States began in Pennsylvania. At the time, Pennsylvania was ruled by the Quakers, who had envisioned their colony as being a sort of multicultural utopia. Germans were thought of as being highly skilled farmers, and thus the Quakers welcomed them in with open arms. Oftentimes, entire families would be transplanted, and they would be given large grants of land that would become multigenerational farms. The descendants of this first group would be called the "Pennsylvania Dutch."

As the western frontiers opened up, many of these people would push westward, into what we now call the Midwest. As you can see in this map of reported ancestry, it kind of looks like self-identified Germans started in Pennsylvania and spread westward in every which direction from there, and that's basically what happened, at least for this first wave of immigrants.

The SECOND major wave of German Immigrants came in between 1820 and WWI, with a particularly large spike following the aftermath of the failed 1848 Revolutions in Europe. THIS wave of immigrants, for the most part, stayed within the same big cities with the Italian and Irish Communities that you are mentioning. By this point, a portion of it was that there was MUCH less land available, and there were already thriving immigrant communities within all of these big cities. This is the same reason that many Irish and Italian immigrants stayed in those cities as well.

A really important distinction to be made here, though, is that the first wave of German immigrants were coming as some of the first settlers in an area that didn't really have any Europeans in it yet, while the latter group was coming into an industrializing country with cities, factory jobs, and large, developed immigrant communities into which they could easily assimilate.

However, I do want to point out that there is a minor flaw in your question, and that is that not every group of Irish immigrants stayed in the cities. Far from it, actually.

The first flows of Irish immigrants came during the Colonial Era as well. Many as indentured servants, and many Ulster Scots (who we now call the "Scots-Irish") came to settle in western Pennsylvania, and then worked their way west into the Ohio river valley and South down the Appalachian mountains. It's a little complicated and not particularly correct to call the Scots-Irish "Irish," since many of them were Scottish settlers in Ireland, but there were large numbers of Irish people in the mix as well. Many Irish indentured servants would run off, and many formed communities in Appalachia and in the "Great Dismal Swamp" of North Carolina. These people primarily populated the "frontier" of the English colonies, west of the original thirteen states, both in and beyond the Appalachian mountains, and on that same chart I posted would be the people who claim "American ancestry."

A book that I recommend, if just for the parts about settlement patterns and maybe not necessarily the main thesis (which has some flaws), is American Nations by Colin Woodard. It provides a really good general overview of how the United States got "peopled."