I think its really hard to compare the DLR hotels to WDW hotels. In theory, all three of the DLR hotels, including Paradise Pier are deluxe level, not moderate. They all have interior corridors, valet and bell service, room service, full service restaurants and bars, larger rooms and the things one associates with the WDW deluxes. However, they don't have quite same the feel as far as theming and grounds. The GCH comes close with the theming, its very similar to the Wildnerness Lodge, however, it doesn't have the grounds.
Paradise Pier is a beach theme with some Disney touches. Its convenient in that you don't have mulitple buildings and long hallways like the DLH and GCH. Its just one central high rise tower. It has a very cool pool slide and a very boring pool area. Its generally much cheaper than GCH. Each room at the PP has a very nice couch that folds down into a very comfortable twin sized bed.
I have stayed at the DLH six times in the past four years and have never found it to be run down. It is the only one of the three DLR hotels that has grounds. It also has the most dining options, a very nicely themed pool and is generally in the middle on price. It has nice large rooms with lots of nice Disney touches. Many of the rooms have daybeds, if it doesn't and you need an extra bed, they will provide a free rollaway. Its my favorite of the three.
GCH is lovely, its the only one that has balconies. The rooms are furnished in a craftsmen style with dark woods. I don't like dark rooms so that was a turn off to me which is strictly a personal thing. The rooms are also smaller than the ones at PP and DLH. However the balconies are wonderful. Some rooms have daybeds, some have bunkbeds. No rollaways are available, so if you don't get one that has a bunk or daybed, you get a sleeping bag if you need that extra sleeping space. The lobby of the GCH has the wow factor that the deluxe's at WDW have, it was designed by the same architect that did the Wildnerness Lodge and Animal Kingdom Lodge. It is the only hotel at DL designed by Disney. The other two were at one time owned by other companies and then taken over by Disney. So their lobbies don't have that themed wow factor. But the grounds of the DLH are lovely and make up for that in my opinion.
I have been the second week of June three times, crowds are heavy, esp. on the weekends. However, since you are staying onsite, you will have Early Entry each day its offered. Its vital at DL to get to the parks at opening before the locals arrive. So yes, crowds will be a factor, however, its very doable. Staying onsite at this time is really nice since you have EE and the nice pools to escape to during midday. None of the neighboring good neighbor hotels have that so I think your idea of staying onsite will help balance the crowd issues. And the good thing about your time frame is that hours are long, shows are running and nighttime entertainment will be every night. If you went a few weeks earlier, you'd have lower crowds but the hours would be short and the fireworks, Electrical Parade and Fantasmic would only run on the weekends. So to me, you picked a good time to go. Before the really intense crowds of July and early August but when the park is in full gear. It will be hot, but not humid and the evenings are so pleasant. Most nights the
Disneyland will be open until 11:00 or even midnight.
If it were me, I'd look into the DLH and see if you can do your five nights there. But in the end, you cannot make a wrong choice, they are all three lovely hotels.